Extensive genome sequencing efforts and advances in microarray technology have converged to create revolutionary new opportunities for high-throughput analyses of gene expression. Within the context of the Program, gene expression analyses will provide information critical to elucidating the mechanisms by which huntingtin and DNA-binding therapeutic agents alter gene expression. The Gene Expression Profiling Core will support the Program's individual Projects by tracking the expression of thousands of mRNAs simultaneously in the respective experimental systems, thereby identifying the specific gene targets of a given pathological or pharmacologic manipulation. Identifying the gene promoters subject to a particular effect will allow the promoter elements and transcription factor(s) responsible for the change to be elucidated. The Gene Expression Core will provide expertise in the design, execution and analysis of microarray profiling studies and will carry out confirmatory analyses using independent methodologies, such as northern blotting. The Principal Investigator of the Core has extensive experience in microarray based expression analyses, including several previous studies of mouse models of polyglutamine disease.